Variant report

Variant	rs3771246
Chromosome Location	chr2:20411453-20411454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:59475738..59478096-chr2:20410813..20413668,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267131	Chromatin interaction
ENSG00000267280	Chromatin interaction
ENSG00000121068	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10495704	0.92[ASN][1000 genomes]
rs1106111	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11096648	0.89[ASN][1000 genomes]
rs11096649	0.89[ASN][1000 genomes]
rs11096650	0.90[ASN][1000 genomes]
rs12373772	0.84[ASN][1000 genomes]
rs12373819	0.84[ASN][1000 genomes]
rs12464428	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13415389	0.84[ASN][1000 genomes]
rs2002090	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2007340	0.89[ASN][1000 genomes]
rs3732162	0.96[ASN][1000 genomes]
rs3732163	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732164	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755300	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771227	0.85[ASN][1000 genomes]
rs3771229	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3771232	0.93[ASN][1000 genomes]
rs3771233	0.87[ASN][1000 genomes]
rs3771236	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771238	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771239	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771240	0.96[ASN][1000 genomes]
rs3771241	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771243	0.96[ASN][1000 genomes]
rs3771244	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771247	0.84[ASN][1000 genomes]
rs3821219	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57938873	0.84[ASN][1000 genomes]
rs59129757	0.84[ASN][1000 genomes]
rs62109740	0.84[ASN][1000 genomes]
rs62111433	0.84[ASN][1000 genomes]
rs72785203	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785204	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72785206	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7585590	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012841	chr2:20328894-20415168	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1000323	chr2:20336237-20419923	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	esv1846803	chr2:20409322-20427189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20389200-20413600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:20391800-20423200	Weak transcription	Right Atrium	heart
3	chr2:20398000-20412200	Weak transcription	NH-A	brain
4	chr2:20401600-20411800	Weak transcription	Spleen	Spleen
5	chr2:20403200-20412600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr2:20403400-20412000	Genic enhancers	HMEC	breast
7	chr2:20403400-20412400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:20403800-20411800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:20403800-20412400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:20404000-20413600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr2:20404000-20414000	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:20404000-20422400	Weak transcription	Brain Germinal Matrix	brain
13	chr2:20404600-20420800	Enhancers	Stomach Mucosa	stomach
14	chr2:20405000-20411800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr2:20405000-20415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:20405200-20413000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:20405200-20413800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:20405200-20414200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:20405200-20414600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:20405800-20411800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:20405800-20416200	Enhancers	Gastric	stomach
22	chr2:20406200-20412800	Enhancers	GM12878-XiMat	blood
23	chr2:20407000-20412000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:20407200-20412200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr2:20407200-20413000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:20407800-20414800	Enhancers	Colonic Mucosa	Colon
27	chr2:20408000-20412400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:20408000-20412600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr2:20408200-20411800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:20408600-20412000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:20408600-20412200	Weak transcription	NHLF	lung
32	chr2:20408600-20414800	Enhancers	Placenta	Placenta
33	chr2:20408800-20412800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:20408800-20413000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:20408800-20413600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr2:20409000-20411800	Weak transcription	Fetal Lung	lung
37	chr2:20409200-20413000	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:20409400-20411600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr2:20409400-20411600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:20409400-20411600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:20409400-20411600	Weak transcription	Fetal Stomach	stomach
42	chr2:20409400-20414400	Weak transcription	Small Intestine	intestine
43	chr2:20409400-20414800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr2:20409600-20412000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:20409600-20412000	Weak transcription	Pancreas	Pancrea
46	chr2:20409800-20412600	Weak transcription	A549	lung
47	chr2:20409800-20413000	Enhancers	Liver	Liver
48	chr2:20409800-20414800	Weak transcription	Lung	lung
49	chr2:20410400-20416200	Genic enhancers	Fetal Intestine Small	intestine
50	chr2:20410600-20412000	Genic enhancers	HepG2	liver

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